Ensure that the ORACLE_HOME is pointing to the right location in $ORACLE_HOME/bin/emca file.

Rather than installing from scratch, if ORACLE_HOME was copied over from another location, likely it results in wrong location for ORACLE_HOME in several Enterprise Manager (EM) specific scripts and files. It usually happens when the directory structure on the target machine is not identical to the structure on the original/source machine, including the top level directory location where Oracle RDBMS was installed properly using the installer.